391 lines
12 KiB
Plaintext
391 lines
12 KiB
Plaintext
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R Under development (unstable) (2024-04-17 r86441) -- "Unsuffered Consequences"
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Copyright (C) 2024 The R Foundation for Statistical Computing
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Platform: aarch64-unknown-linux-gnu
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R is free software and comes with ABSOLUTELY NO WARRANTY.
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You are welcome to redistribute it under certain conditions.
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Type 'license()' or 'licence()' for distribution details.
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R is a collaborative project with many contributors.
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Type 'contributors()' for more information and
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'citation()' on how to cite R or R packages in publications.
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Type 'demo()' for some demos, 'help()' for on-line help, or
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'help.start()' for an HTML browser interface to help.
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Type 'q()' to quit R.
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> # Tests of pseudovalues, by calculating directly from survfit and residuals
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> # this assumes that residuals.survfit is correct
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> library(survival)
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> aeq <- function(x, y, ...) all.equal(as.vector(x), as.vector(y), ...)
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>
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> mdata <- mgus2
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> temp <- ifelse(mdata$pstat==1, 1, 2*mdata$death)
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> mdata$event <- factor(temp, 0:2, c("censor", "pcm", "death"))
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> mdata$etime <- ifelse(mdata$pstat==1, mdata$ptime, mdata$futime)
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> mdata <- subset(mdata, etime > 12) # remove first year
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> tvec <- c(10, 100, 200, 365)
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>
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> # Single endpoint, one curve
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> fit1 <- survfit(Surv(ptime, pstat) ~1, mdata)
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> # a time point before first event, after last event, at an event time,
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> # and between event times
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> rr1 <- resid(fit1, tvec)
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> aeq(colSums(rr1), rep(0,4))
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[1] TRUE
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> sv1 <- summary(fit1, time=tvec, extend=TRUE)$surv
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>
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> # one time point
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> ps1a <- pseudo(fit1, time=100)
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> aeq(ps1a, sv1[2] + fit1$n*rr1[,2])
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[1] TRUE
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> # multiple
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> ps1b <- pseudo(fit1, time=tvec)
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> aeq(ps1b, sv1[col(rr1)] + fit1$n * rr1)
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[1] TRUE
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>
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> # Single endpoint, multiple curves
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> fit2 <- survfit(Surv(futime, death) ~ sex, mdata)
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> rr2 <- resid(fit2, time=tvec)
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> aeq(colSums(rr2), rep(0,4))
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[1] TRUE
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> sv2 <- summary(fit2, time=tvec, extend=TRUE)$surv
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> sv2 <- t(matrix(sv2, ncol=2)) # row 1= female, row2 = male
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>
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> # residuals are the same as for separate models
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> fit2a <- survfit(Surv(futime, death) ~1, mdata, subset=( sex=='F'))
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> fit2b <- survfit(Surv(futime, death) ~1, mdata, subset= (sex=='M'))
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> fem <- (mdata$sex=='F')
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> rr2a <- resid(fit2a, times=tvec)
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> rr2b <- resid(fit2b, times=tvec)
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> aeq(rr2a, rr2[fem,]) # row names won't be equal
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[1] TRUE
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> aeq(rr2b, rr2[!fem,])
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[1] TRUE
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>
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> # one time point
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> ps2a <- pseudo(fit2a, time=100)
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> aeq(ps2a, sv2[1,2] + fit2a$n[1]* rr2a[,2])
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[1] TRUE
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> ps2b <- pseudo(fit2b, time=100)
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> aeq(ps2b, sv2[2,2] + fit2b$n[1]* rr2b[,2])
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[1] TRUE
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>
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> # overall psuedo are the same as for separate models
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> # (each row of mdata belongs to a single curve)
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> ps2c <- pseudo(fit2, time=100)
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> aeq(ps2c[ fem], ps2a)
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[1] TRUE
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> aeq(ps2c[!fem], ps2b)
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[1] TRUE
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>
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> # multiple time points
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> ps2d <- pseudo(fit2a, times=tvec)
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> aeq(ps2d, sv2[1, col(rr2a)] + fit2$n[1]* rr2a)
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[1] TRUE
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> ps2e <- pseudo(fit2b, times=tvec)
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> aeq(ps2e, sv2[2, col(rr2b)] + fit2$n[2]* rr2b)
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[1] TRUE
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>
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> ps2f <- pseudo(fit2, times=tvec)
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> aeq(ps2d, ps2f[ fem,])
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[1] TRUE
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> aeq(ps2e, ps2f[!fem,])
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[1] TRUE
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>
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> # Repeat the process for a multi-state model
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> fit3 <- survfit(Surv(etime, event) ~ sex, mdata)
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> fit3a <- survfit(Surv(etime, event) ~1, mdata, subset= (sex=='F'))
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> fit3b <- survfit(Surv(etime, event) ~1, mdata, subset= (sex=='M'))
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> rr3 <- resid(fit3, times=tvec)
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> aeq(apply(rr3, 2:3, sum), matrix(0,3,4)) # resids sum to 0 for each state & time
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[1] TRUE
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> rr3a <- resid(fit3a, times=tvec)
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> rr3b <- resid(fit3b, times=tvec)
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> aeq(rr3[fem,,], rr3a)
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[1] TRUE
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> aeq(rr3[!fem,,], rr3b)
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[1] TRUE
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>
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> ps3 <- pseudo(fit3, times=tvec)
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> ps3a <- pseudo(fit3a, times=tvec)
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> ps3b <- pseudo(fit3b, times=tvec)
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> aeq(ps3[ fem,,], ps3a)
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[1] TRUE
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> aeq(ps3[!fem,,], ps3b)
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[1] TRUE
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>
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> sv3 <- summary(fit3, times=tvec, extend=TRUE)$pstate
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> sv3 <- array(sv3, dim=c(4,2,3)) #times, curve, order
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> # ps3a has dimensions (number obs in fit3a, 3 states, 4 timepoints)
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> # to each of the 3x4 combinations we need to add the value of the
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> # survival curve at that time. A loop is easiest
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> temp1 <- array(0, dim= dim(rr3a))
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> temp2 <- array(0, dim= dim(rr3b))
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> for (i in 1:3) { # each of the 3 states
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+ for (j in 1:4) { # each of the 4 times
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+ temp1[, i,j] <- sv3[j,1,i] + fit3$n[1]*rr3a[,i,j]
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+ temp2[, i,j] <- sv3[j,2,i] + fit3$n[2]*rr3b[,i,j]
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+ }
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+ }
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> aeq(temp1, ps3a)
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[1] TRUE
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> aeq(temp2, ps3b)
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[1] TRUE
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>
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> ###########################
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> # All again, just the same, for cumulative hazards
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> # Though there are 2 of them, vs 3 states.
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> #
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> rr1 <- resid(fit1, tvec, type="cumhaz")
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> aeq(colSums(rr1), rep(0,4))
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[1] TRUE
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> sv1 <- summary(fit1, time=tvec, extend=TRUE)$cumhaz
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>
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> # one time point
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> ps1a <- pseudo(fit1, time=100, type="cumhaz")
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> aeq(ps1a, sv1[2] + fit1$n*rr1[,2])
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[1] TRUE
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> # multiple
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> ps1b <- pseudo(fit1, time=tvec, type="cumhaz")
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> aeq(ps1b, sv1[col(rr1)] + fit1$n * rr1)
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[1] TRUE
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>
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> # Single endpoint, multiple curves
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> fit2 <- survfit(Surv(futime, death) ~ sex, mdata)
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> rr2 <- resid(fit2, time=tvec, type="cumhaz")
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> aeq(colSums(rr2), rep(0,4))
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[1] TRUE
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> sv2 <- summary(fit2, time=tvec, extend=TRUE)$cumhaz
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> sv2 <- t(matrix(sv2, ncol=2)) # row 1= female, row2 = male
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>
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> # residuals are the same as for separate models
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> rr2a <- resid(fit2a, times=tvec, type= "cumhaz")
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> rr2b <- resid(fit2b, times=tvec, type= "cumhaz")
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> aeq(rr2a, rr2[fem,])
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[1] TRUE
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> aeq(rr2b, rr2[!fem,])
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[1] TRUE
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>
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> # one time point
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> ps2a <- pseudo(fit2a, time=100, type="cumhaz")
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> aeq(ps2a, sv2[1,2] + fit2a$n[1]* rr2a[,2])
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[1] TRUE
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> ps2b <- pseudo(fit2b, time=100, type="cumhaz")
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> aeq(ps2b, sv2[2,2] + fit2b$n[1]* rr2b[,2])
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[1] TRUE
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>
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> # overall psuedo are the same as for separate models
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> # (each row of mdata belongs to a single curve)
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> ps2c <- pseudo(fit2, time=100, type="cumhaz")
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> aeq(ps2c[ fem], ps2a)
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[1] TRUE
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> aeq(ps2c[!fem], ps2b)
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[1] TRUE
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>
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> # multiple time points
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> ps2d <- pseudo(fit2a, times=tvec, type="cumhaz")
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> aeq(ps2d, sv2[1, col(rr2a)] + fit2$n[1]* rr2a)
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[1] TRUE
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> ps2e <- pseudo(fit2b, times=tvec, type= "cumhaz")
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> aeq(ps2e, sv2[2, col(rr2b)] + fit2$n[2]* rr2b)
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[1] TRUE
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>
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> ps2f <- pseudo(fit2, times=tvec, type="cumhaz")
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> aeq(ps2d, ps2f[ fem,])
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[1] TRUE
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> aeq(ps2e, ps2f[!fem,])
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[1] TRUE
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>
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> # Repeat the process for a multi-state model
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> rr3 <- resid(fit3, times=tvec, type="cumhaz")
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> aeq(apply(rr3, 2:3, sum), matrix(0, 2,4))
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[1] TRUE
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> rr3a <- resid(fit3a, times=tvec, type="cumhaz")
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> rr3b <- resid(fit3b, times=tvec, type="cumhaz")
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> aeq(rr3[fem,,], rr3a)
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[1] TRUE
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> aeq(rr3[!fem,,], rr3b)
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[1] TRUE
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>
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> ps3 <- pseudo(fit3, times=tvec, type="cumhaz")
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> ps3a <- pseudo(fit3a, times=tvec, type="cumhaz")
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> ps3b <- pseudo(fit3b, times=tvec, type="cumhaz")
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> aeq(ps3[ fem,,], ps3a)
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[1] TRUE
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> aeq(ps3[!fem,,], ps3b)
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[1] TRUE
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>
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> sv3 <- summary(fit3, times=tvec, extend=TRUE)$cumhaz
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> sv3 <- array(sv3, dim=c(4,2,2)) #times, curve, hazard
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> # ps3a has dimensions (number obs in fit3a, 4 timepoints, 3 states)
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> # to each of the 4x3 combinations we need to add the value of the
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> # survival curve at that time. A loop is easiest
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> temp1 <- array(0, dim= dim(rr3a))
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> temp2 <- array(0, dim= dim(rr3b))
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> for (i in 1:2) { # each of the 2 hazard
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+ for (j in 1:4) { # each of the 4 timepoints
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+ temp1[, i,j] <- sv3[j,1,i] + fit3$n[1]*rr3a[,i,j]
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+ temp2[, i,j] <- sv3[j,2,i] + fit3$n[2]*rr3b[,i,j]
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+ }
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+ }
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> aeq(temp1, ps3a)
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[1] TRUE
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> aeq(temp2, ps3b)
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[1] TRUE
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>
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> #################################################
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> # Last, one more time with AUC
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> # A bit more bother, since summary.survfit only returns AUC for one time
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> # value at a time. It also does not like times before the first event
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> #
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> tvec <- tvec[2:4]
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>
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> rr1 <- resid(fit1, tvec, type="auc")
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> aeq(colSums(rr1), rep(0,3))
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[1] TRUE
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> afun <- function(fit, times) {
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+ ntime <- length(times)
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+ if (length(fit$strata)) xfun <- function(x) x$table[, "rmean"]
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+ else xfun <- function(x) x$table["rmean"]
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+
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+ temp <- xfun(summary(fit, rmean=times[1]))
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+ if (ntime==1) return(temp)
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+
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+ result <- matrix(0, ntime, length(temp))
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+ result[1,] <- temp
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+ for (i in 2:ntime)
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+ result[i,] <- xfun(summary(fit, rmean=times[i]))
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+ drop(result)
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+ }
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>
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> sv1 <- afun(fit1, tvec)
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>
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> # one time point
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> ps1a <- pseudo(fit1, time=tvec[1], type="auc")
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> aeq(ps1a, sv1[1] + fit1$n*rr1[,1])
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[1] TRUE
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> # multiple
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> ps1b <- pseudo(fit1, time=tvec, type="auc")
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> aeq(ps1b, sv1[col(rr1)] + fit1$n * rr1)
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[1] TRUE
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>
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> # Single endpoint, multiple curves
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> rr2 <- resid(fit2, time=tvec, type="auc")
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> sv2 <- t(afun(fit2, tvec))
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> aeq(colSums(rr2), rep(0,3))
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[1] TRUE
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>
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> # residuals are the same as for separate models
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> rr2a <- resid(fit2a, times=tvec, type= "auc")
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> rr2b <- resid(fit2b, times=tvec, type= "auc")
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> aeq(rr2a, rr2[fem,])
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[1] TRUE
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> aeq(rr2b, rr2[!fem,])
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[1] TRUE
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>
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> # one time point
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> ps2a <- pseudo(fit2a, time=100, type="auc")
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> aeq(ps2a, sv2[1,1] + fit2a$n[1]* rr2a[,1])
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[1] TRUE
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> ps2b <- pseudo(fit2b, time=100, type="auc")
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> aeq(ps2b, sv2[2,1] + fit2b$n[1]* rr2b[,1])
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[1] TRUE
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>
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> # overall psuedo are the same as for separate models
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> # (each row of mdata belongs to a single curve)
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> ps2c <- pseudo(fit2, time=100, type="auc")
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> aeq(ps2c[ fem], ps2a)
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[1] TRUE
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> aeq(ps2c[!fem], ps2b)
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[1] TRUE
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>
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> # multiple time points
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> ps2d <- pseudo(fit2a, times=tvec, type="auc")
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> aeq(ps2d, sv2[1, col(rr2a)] + fit2$n[1]* rr2a)
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[1] TRUE
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> ps2e <- pseudo(fit2b, times=tvec, type= "auc")
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> aeq(ps2e, sv2[2, col(rr2b)] + fit2$n[2]* rr2b)
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[1] TRUE
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>
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> ps2f <- pseudo(fit2, times=tvec, type="auc")
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> aeq(ps2d, ps2f[ fem,])
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[1] TRUE
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> aeq(ps2e, ps2f[!fem,])
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[1] TRUE
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>
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> # Repeat the process for a multi-state model
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> rr3 <- resid(fit3, times=tvec, type="auc")
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> aeq(apply(rr3, 2:3, sum), matrix(0, 3,3))
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[1] TRUE
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> rr3a <- resid(fit3a, times=tvec, type="auc")
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> rr3b <- resid(fit3b, times=tvec, type="auc")
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> aeq(rr3[fem,,], rr3a)
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[1] TRUE
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> aeq(rr3[!fem,,], rr3b)
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[1] TRUE
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>
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> ps3 <- pseudo(fit3, times=tvec, type="auc")
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> ps3a <- pseudo(fit3a, times=tvec, type="auc")
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> ps3b <- pseudo(fit3b, times=tvec, type="auc")
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> aeq(ps3[ fem,,], ps3a)
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[1] TRUE
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> aeq(ps3[!fem,,], ps3b)
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[1] TRUE
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>
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> sv3 <- rbind(summary(fit3, rmean=tvec[1])$table[,"rmean"],
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+ summary(fit3, rmean=tvec[2])$table[,"rmean"],
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+ summary(fit3, rmean=tvec[3])$table[,"rmean"])
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> sv3 <- array(sv3, dim=c(3,2,3)) #times, curve, state
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> # ps3a has dimensions (number obs in fit3a, 4 timepoints, 3 states)
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> # to each of the 4x3 combinations we need to add the value of the
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> # survival curve at that time. A loop is easiest
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> temp1 <- array(0, dim= dim(rr3a))
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> temp2 <- array(0, dim= dim(rr3b))
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> for (i in 1:3) { # each of the 3 states
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+ for (j in 1:3) { # each of the 3 times
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+ temp1[, i,j] <- sv3[j,1,i] + fit3$n[1]*rr3a[,i,j]
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+ temp2[, i,j] <- sv3[j,2,i] + fit3$n[2]*rr3b[,i,j]
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+ }
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+ }
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> aeq(temp1, ps3a)
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[1] TRUE
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> aeq(temp2, ps3b)
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[1] TRUE
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>
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> #
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> # a data set with a missing value, and with a group that has only one obs
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> # a good test of edge cases
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> #
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> lfit1 <- survfit(Surv(time, status) ~ ph.ecog, lung)
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> # This will warn about points beyond the curve; ph.ecog==3 has a single point
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> # at time=118, and it will have one fewer obs than the data
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> p1 <- pseudo(lfit1, times=c(100, 200))
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Warning message:
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In pseudo(lfit1, times = c(100, 200)) :
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requested time points are beyond the end of one or more curves
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> aeq(dim(p1), c(nrow(lung)-1, 2))
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[1] TRUE
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>
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>
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> # This will have rows that match the data
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> lfit2 <- survfit(Surv(time, status) ~ ph.ecog, lung, na.action= na.exclude)
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> p2 <- pseudo(lfit2, time=c(100, 200))
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Warning message:
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In pseudo(lfit2, time = c(100, 200)) :
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requested time points are beyond the end of one or more curves
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> aeq(dim(p2), c(nrow(lung), 2))
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[1] TRUE
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> all(is.na(p2[is.na(lung$ph.ecog)])) # a row of missing was inserted
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[1] TRUE
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>
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> row3 <- which(!is.na(lung$ph.ecog) & lung$ph.ecog ==3) # the singleton row
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> all(p2[row3,] == c(1, 0))
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[1] TRUE
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>
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>
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> proc.time()
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user system elapsed
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0.622 0.024 0.643
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